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Junqueras completed his primary and secondary education at an Italian school in Barcelona. He began his university education studying economics at the University of Barcelona, but went on to earn an undergraduate degree in Modern and Contemporary History and a doctorate in History of Economic Thought from the Autonomous University of Barcelona.[2] His thesis analyzed the origins of modern economic thought in the western Mediterranean, establishing appropriate parallels with English and Castilian thought in the first decades of the seventeenth century.

He is a professor in the Department of Modern and Contemporary History at the Autonomous University of Barcelona and has contributed to a variety of Catalan radio and television programs related to history.

Junqueras headed ERC's electoral list for the 2009 European elections. He appeared on the list as an independent, despite serving on the town council of Sant Vicenç dels Horts as a member of ERC. Junqueras won a seat in the European Parliament as part of the group The Greens–European Free Alliance.

Junqueras became a member of the Parliament of Catalonia following the election held on 25 November 2012. He is the president of the Republican Left of Catalonia's parliamentary group.[3] On 19 December 2012, following weeks of negotiations between their parties, Junqueras and Artur Mas, the president of Convergence and Union, signed a "governability agreement". The agreement includes a commitment to hold a referendum in 2014 on whether Catalonia should separate from Spain.[4] The Republican Left of Catalonia agreed to provide Mas with the additional parliamentary votes he needed to be reelected President of the Generalitat and guarantee the stability of his government, receiving concessions to its economic and political program in return. In January 2013 Núria de Gispert, president of the Parliament of Catalonia, named Junqueras Leader of the Opposition, despite the objections of the Socialists' Party of Catalonia and Initiative for Catalonia Greens, who argued that this position could not be held by the leader of a party that had a "governability agreement" with the governing party.[5]